01 jetta running rough after water pump changed

I have a 01 jetta glx/vr6.  approx 2 months ago i was beginning to to see signs my water pump was failing while at work.  i filled the reservoir up and drove it home(1mile).  The car then sat in the driveway till i could afford to fix it, plus with weather still good i decided to start walking to work.  after 2 months and the weather changing, i changed the water pump without any issues.  we disconnected coolant reservoir, removed the washer reservoir and pump, and disconnected the engine mount on the left side of the engine, and slowly lowered the engine to gain access from below to the water pump.  everything was fine, we changed out the water pump. (no signs of anything broken off or missing). we replaced everything and attempted to start the car.  due to the car not running for 2 months the battery had died, and needed to be jumped.  when the car finally started (2-4 times trying) it ran horribly, sounding as if was misfiring.  after removal of each plug wire, there was a noticeable change in the engine(so not spark plugs or wires) the engine continued to run poorly. we rechecked all wires and hoses, but could not find anything unplugged or miss connected.  I am at a loss, if anyone can give me a direction or has run into this before, please let me know.  Any help would be grateful.